splatPopParseEmpirical {splatter} | R Documentation |
Parse splatPop key information from empirical data provided.
splatPopParseEmpirical( vcf = vcf, gff = gff, eqtl = eqtl, means = means, params = params )
vcf |
VariantAnnotation object containing genotypes of samples. |
gff |
Either NULL or a data.frame object containing a GFF/GTF file. |
eqtl |
Either NULL or if simulating population parameters directly from empirical data, a data.frame with empirical/desired eQTL results. To see required format, run 'mockEmpiricalSet()' and see eqtl output. |
means |
Either NULL or if simulating population parameters directly from empirical data, a Matrix of real gene means across a population, where each row is a gene and each column is an individual in the population. To see required format, run 'mockEmpiricalSet()' and see means output. |
params |
SplatPopParams object containing parameters for population
scale simulations. See |
NOTE: This function will cause some of the parameters in the splatPopParams object to be ignored, such as population level gene mean and variance and eQTL parameters.
This function will ignore a number of parameters defined in splatPopParams, instead pulling key information directly from provided VCF, GFF, gene means, and eQTL mapping result data provided.
A partial splatPop 'key'